One of the longstanding challenges in infectious disease has been the lack of high-quality reference genomes. However, developments in genome sequencing are helping researchers overcome this barrier. Recently, highly contiguous genome assemblies of Plasmodium falciparum, Aedes aegypti, and multiple trypanosomes have become available. The number of reference genomes for bacteria that cause infectious disease is similarly expanding rapidly. In this webinar Meredith Ashby discusses how these new resources are already yielding new biological insights into critical questions in infectious disease research, including how parasites evade the immune system add how pathogens are adapting to evolutionary pressures.
In this PacBio User Group Meeting presentation, Mount Sinai’s Ethan Ellis presents results from the HLS-CATCH method, which involves the use of the SageHLS instrument with CRISPR design methods to target and extract large genomic fragments for sequencing while avoiding pseudogenes and other confounding regions.
In this PacBio User Group Meeting presentation, Eugenio Daviso from Covaris talks about the use of adaptive focused acoustics for gentle cell lysis and extraction of high molecular weight DNA.
In this PacBio User Group Meeting presentation, PacBio scientist Kristin Mars speaks about recent updates, such as the single-day library prep that’s now possible with the Iso-Seq Express workflow. She also notes that one SMRT Cell 8M is sufficient for most Iso-Seq experiments for whole transcriptome sequencing at an affordable price.
In this presentation at PAG 2020, Bart Nijland of Genetwister Technologies explains how his team set out to make a haplotype-aware assembly of the highly complex tetraploid Rosa x hybrida L. genome in order to capture its full range of genetic variation. HiFi reads generated from PacBio’s Sequel II System have made it possible to parse out critical information from many of the plant’s parental genes.
In this PacBio User Group Meeting presentation, Shawn Trojahn of Washington State University describes transcriptome sequencing and analysis of grizzly bears focused on differential gene expression during hibernation and active cycles, potentially offering human-relevant information about muscle atrophy and insulin resistance. The team was able to identify more unique isoforms just from liver tissue than had been previously characterized in the entire reference genome. Of particular interest: more than 2,000 transcripts differentially expressed between hibernation and active season, including 86 genes that have isoforms expressed in opposite directions.
In this PacBio User Group Meeting lightning talk, NEB’s Kelly Zatopek shares data from RADAR-seq, an amplification-free method for detecting and quantifying a wide variety of DNA damage types across a genome.
Mark Blaxter, project lead of the Sanger Institute’s Darwin Tree of Life, shared an update of the ambitious effort to sequence all 60,000 species believed to be on the British Isles over the next 12 years in this presentation at the PAG 2020 Conference. The Sanger team has already generated data for 94 species, including 44 new moth and butterfly (Lepidoptera) PacBio assemblies, which Blaxter describes in this presentation.
In this PacBio User Group Meeting presentation, Nic Wheeler of University of Wisconsin-Madison, speaks about RNA sequencing for filarial nematodes associated with understudied tropical diseases. His team used Iso-Seq analysis to improve gene models and achieve better transcriptome coverage for these worms, which typically have poorly annotated and fragmented genome assemblies. While getting enough RNA to study is a technical challenge, the group still managed to generate full-length isoforms, many of which were novel or contained novel junctions.
During a PAG 2020 workshop, Zev Kronenberg, a senior bioinformatics engineer at PacBio, describes how he used the PacBio Iso-Seq transcriptome sequencing and analysis method to annotate great ape genomes, detangle several complicated loci, and enrich our biological understanding of the differences between apes and humans.
In this PacBio User Group Meeting presentation, Mitchell Vollger of the University of Washington used HiFi reads from SMRT Sequencing to study segmental duplications in the human genome. The technique significantly reduced the complexity of accurately mapping these nearly identical sequences throughout the genome; it also reduced the amount of compute power needed compared to a previous PacBio assembly using continuous long reads instead of circular consensus sequencing. Despite generating less data with the HiFi assembly, the team still resolved 30% more segmental duplications with the new approach.
In this webinar we present Single Molecule, Real-Time (SMRT) Sequencing and the Iso-Seq method, which allow you to generate full-length cDNA sequences — no assembly required — to characterize transcript isoforms within targeted genes or across an entire transcriptome. The presenters share how the Iso-Seq method: (1) Provides high quality, full-length transcript sequences of up to 15 kb; (2) Allows for one-day library prep on a single SMRT Cell 8M to comprehensively characterize a whole transcriptome; (3) Facilitates discovery of alternative splicing events, fusion gene detection, and allelic specific isoform detection; and (4) Enables discovery of potential cancer-specific isoforms in…
In this PacBio User Group Meeting lightning talk, Shawn Polson of the University of Delaware speaks about viral metagenomes, which are more challenging to distinguish than their bacterial counterparts because viruses have no 16S equivalent. By using SMRT Sequencing, his team generated higher-resolution data about viral genomes and aims to use this information as a guide to how these genomes function.
Understanding interactions among plants and the complex communities of organisms living on, in and around them requires more than one experimental approach. A new method for de novo metagenome assembly, PacBio HiFi sequencing, has unique strengths for determining the functional capacity of metagenomes. With HiFi sequencing, the accuracy and median read length of unassembled data outperforms the quality metrics for many existing assemblies generated with other technologies, enabling cost-competitive recovery of full-length genes and operons even from rare species. When paired with the ability to close the genomes of even challenging isolates like Xanthomonas, the PacBio Sequel II System is…
In this PacBio User Group Meeting lightning talk, Alexandra Pike of MIT presents a study of TIN2, a telomere-binding protein, which is mutated in some short telomere syndromes. By pairing the Iso-Seq method with CRISPR, her team revealed a previously uncharacterized TIN2 isoform that may have a functional difference for individuals with these syndromes.